Table 1.
Global biological functional comparison of fenretinide and all-trans RA based on gene expression.
| David biological functional annotationa | Fenretinide-regulated genes | RXRα-Bound Genes (%) | p value | All-trans RA- regulated genes | RXRα-Bound Genes (%) | p value |
|---|---|---|---|---|---|---|
|
preferentially regulated by fenretinide
| ||||||
| lipid biosynthetic process | 44 | 30 (68%) | 1.1E-07 | 0 | ||
| fatty acid metabolic process | 26 | 18 (69%) | 1.2E-04 | 0 | ||
| carboxylic acid biosynthetic process (organic acid) | 23 | 18 (78%) | 5.4E-05 | 0 | ||
| carboxylic acid transport (organic acid) | 22 | 18 (82%) | 7.2E-05 | 0 | ||
| amino acid transport | 16 | 14 (88%) | 1.4E-04 | 0 | ||
|
| ||||||
|
preferentially regulated by all-trans RA
| ||||||
| regulation of transcription from RNA polymerase II promoter | 0 | 156 | 130 (83%) | 6.6E-07 | ||
| cellular response to stress | 0 | 126 | 96 (76%) | 1.3E-06 | ||
| DNA metabolic process | 0 | 115 | 85 (74%) | 7.9E-07 | ||
| negative regulation of transcription | 0 | 98 | 89 (91%) | 1.2E-04 | ||
| regulation of locomotion (cell motion) | 0 | 55 | 50 (91%) | 6.2E-06 | ||
| nuclear division (mitosis) | 0 | 54 | 35 (65%) | 8.2E-05 | ||
| response to protein stimulus | 0 | 33 | 25 (76%) | 4.6E-05 | ||
| response to unfolded protein | 0 | 24 | 17 (71%) | 1.4E-04 | ||
|
| ||||||
|
Common processes regulated by fenrentinide and all-trans RA
| ||||||
| cell cycle | 100 | 80 (80%) | 7.2E-08 | 231 | 123 (53%) | 5.7E-13 |
| response to organic substance | 80 | 68 (85%) | 6.1E-09 | 176 | 144 (82%) | 3.2E-12 |
| regulation of cell proliferation | 74 | 60 (81%) | 1.4E-05 | 179 | 159 (89%) | 5.5E-10 |
| regulation of apoptosis | 74 | 67 (91%) | 2.8E-05 | 239 | 190 (80%) | 4.6E-08 |
| oxidation reduction | 62 | 48 (77%) | 3.0E-05 | 132 | 107 (81%) | 3.7E-05 |
| response to wounding | 51 | 44 (86%) | 2.1E-04 | 114 | 100 (88%) | 2.3E-05 |
| response to endogenous stimulus | 47 | 39 (83%) | 4.0E-06 | 100 | 81 (81%) | 1.4E-07 |
| response to extracellular stimulus | 35 | 31 (89%) | 6.9E-08 | 65 | 51 (79%) | 3.1E-08 |
| response to nutrient levels | 34 | 30 (88%) | 1.5E-08 | 62 | 49 (79%) | 5.0E-09 |
| steroid (sterol) metabolic process | 34 | 18 (53%) | 2.7E-08 | 58 | 44 (76%) | 5.3E-07 |
| cholesterol metabolic process | 21 | 16 (76%) | 1.4E-07 | 30 | 21 (70%) | 3.6E-05 |
| steroid (sterol) biosynthetic process | 23 | 15 (65%) | 1.0E-09 | 28 | 16 (57%) | 5.6E-05 |
| cholesterol biosynthetic process | 14 | 10 (71%) | 2.6E-10 | 15 | 8 (53%) | 3.8E-06 |
| response to vitamin | 14 | 12 (86%) | 6.4E-05 | 24 | 21 (88%) | 3.9E-05 |
| glutamine family amino acid metabolic process | 12 | 12 (100%) | 1.2E-04 | 21 | 19 (91%) | 2.4E-05 |
a
Biological processes were obtained from DAVID function annotation.